Xiaofei Zeng

Hi, Kun There's nothing wrong with your commands. You could try using the parameter `--skip_allhic` in `haphic sort`. It will help me figure out whether the problem occurred during ALLHiC...

Hi Kun, I'm glad to see that your result has improved significantly. I also have a plan to fix the issue raised by ALLHiC. In group5, there could be a...

Hi Kun, Thanks for your suggestion! I will improve it in the subsequent updates. Best regards, Xiaofei

> Hi, Xiaofei > > Just a suggestion. > > Would you please don't change contig names in final agp file when running pipeline with `--correct_nrounds (>0)` options, use original...

In the latest commit of HapHiC, I have fixed a bug which can lead to a Segmentation fault in running `juicebox.sh`. Xiaofei

Yes, to install a newer version of sklearn, you should `pip3 install scikit-learn`, just like what we did in https://github.com/zengxiaofei/HapHiC/blob/main/conda_env/create_conda_env_py311.sh: ```bash conda create -n haphic_py311 python=3.11.2 conda activate haphic_py311 pip3...

Hi Kun, Thanks! I have fixed this bug in the latest commit. Best regards, Xiaofei

Hi @ZJ-1992, The anchoring rate is controlled by several parameters including `--min_RE_sites`, `--min_links`, `--min_link_density`, and `--min_density_ratio`. Unfortunately, determining the thresholds of these parameters is still challenging until the heatmap is...

In the [latest commit](https://github.com/zengxiaofei/HapHiC/commit/f4e81362f76fed2e080bdb25a5bdd0a1b40486a5), I improved the stability of contig ordering and orientation by comparing the results of fast sorting with ALLHiC optimization and selecting the better one.

@zy66-su, It's hard to tell whether these regions were correctly assembled or not using a Hi-C contact map. Hi-C reads that are mapped to such regions are often filtered out...